It depends on what you want to do in your game.
If you are going for WC, then you don't need manufacturies (though if you've gotten your full support built out, why not?) Just build the men and conquer.
If you are territorially constrained, manufactories are generally a good deal, but there are other investments to be had that may be better. Are you dominating world trade yet? Got all your same-culture or pagan provinces converted? Promoted all officials? And even if you are BB-constrained, you should consider trying to swap your lower value provinces for higher value ones. I.e., find a defensive war where you can easily get a gold province, and take it, then free a vassal. This may be a good investment depending on how many troops you lose taking the gold province.
BTW, building refineries tends to be profitable long after the other manufacturies aren't, because world trade will be worth many thousands, of which you should be getting perhaps 40%. So, adding 1% to TE, in addition to making your merchants stickier, is going to be worth a lot; later in the game this can easily be more than the 60 in trade investment that the refinery makes. And it keeps increasing as colonization happens. Goods manufacturies are similarly a good deal if you are doing WC, though I think production and trade tend to be about the same, and you can dominate world trade long before you can dominate a similar fraction of world production.
